By Mohammed Akel (Spring 2023)
The following page utilizes different ways of evaluating Nanome's immersive virtual reality features. First, it presents findings from a brief literature review and evidence synthesis. Second, it presents essential findings and insights from Nanome's in-class activity conducted by Mohammed Akel (the activity took place on 28/02/2023 at Brown's Computer Science Department). Third, it provides a brief analysis and comparison of molecular visualization in 2D vs 3D as well as desktop vs immersive visualizations. Finally, it looks at some of the available comparable models in the market.
As a refresher, Nanome is a software platform, founded in 2015, that uses virtual reality and other advanced technologies to enable scientific data visualization as well as manipulation of molecules and other complex chemical data in an immersive 3D environment. Nanome also allows for the visualization of correlations between different chemical and biological structures. It includes remote collaboration tools and features integrations that enable data connectivity with other pharmaceutical systems.
Part 01: Literature Review
A brief literature review shows that there is significant hype about platforms like Nanome; Platforms like Nanome seem to hold incredible potential for the healthcare and pharmaceutical industry, saving organizations lots of dollars, time, and energy every year. It is important to keep in mind that the domain of immersive molecular visualization is still rather new, and there are no long-term established procedures for the evaluation of the presented results; However, a number of studies have been conducted that dwell on the possibilities and potential of platforms like Nanome. The section below summarizes the findings of some of the notable studies as well as provide resources for constructively exploring the literature around Nanome:
Accelerating drug discovery to create a healthier future: A Case Study on using Nanome by Nimbus Therapeutics
Nimbus Therapeutics focuses on early-stage drug discovery and development with the goal of creating life-changing medicines
The study revealed that Nanome could help shorten the average 12–18 month lead optimization timeline for new drugs
VR visualizations enhance communication between the computational chemists designing the chemical structures and the synthetic chemists and biologists who take over from there
Development of a virtual reality platform for effective communication of structural data in drug discovery by J. Kingsley et al
Kingsley et al. present the architecture of the tool, three proposed collaborative modes, and a demonstration of its usage in designing a small molecular structure
Reflects on how Nanome’s immersive 3D environment allows users to better understand structural features and nuances
Illustrates the importance of cross-site collaboration and molecular editing of structural data in Nanome
Emphasizes the importance of Nanome’s intuitive design and ease of use philosophy
A number of other studies can be found here.
Another way of looking at the available literature to informally evaluate Nanome's platform could be to look at what Nanome’s clients have to say about the platform and its different features. Many biotech and pharmaceutical companies are utilizing Nanome’s features to accelerate their processes and optimize the resources available. The section below looks at the testimonies of the most notable biotech companies utilizing Nanome within their business activities:
Uses Nanome at the computational platform for drug discovery to generate dynamic 3D information about proteins and biomolecular systems, which they use to predict molecular properties and drive decisions in their drug discovery projects
Argues that seeing molecules in virtual reality (VR) brings a depth of understanding to their scientists that has previously been inaccessible
Claims that Nanome’s insights, especially when coupled with accurate predictive simulations, can lead to project breakthroughs and accelerate progress toward the clinic
Argues that Nanome helps them with a better understanding of the 3D molecular structures, giving new insights into ways that a candidate drug might interact with its protein target
Argues that Nanome brought a new point of view to the team and introduced a new way to analyze 3D problems
Click here for more testimonies from Nanome's clients.
Overall, the literature suggests that Nanome has the potential to revolutionize the way scientists and researchers interact with complex scientific data, enabling them to visualize and manipulate molecules and other structures in three dimensions, and to collaborate with colleagues remotely. Its potential applications are vast, ranging from drug discovery and materials science to education and training.
Part 02: Insights from Mohammed's In-class activity
During the in-class activity conducted on 28/02/2023, 12 users were asked to complete a form evaluating their experiences with the platform, its features, collaboration tools, and overall user likability. The section below presents the findings and insights observed. A detailed description of the In-class activity can be found here. An evaluation brief can be found here.
91% of the users said that Basics Tutorials were helpful
36% of the users expressed it was easy to join a public room
67% of the users found the COVID-19 Main Protease visualization to be helpful while 54% found the COVID-19 Spike Protein visualization to be helpful
18% of users said they will not be exploring the app further
Users favorite tools
Overall, users really appreciated the potential the platform has to offer. Due to technical difficulties during the activity, it may not be best suited for evaluating elements of collaboration. In addition, many users expressed that more contextual information about the COVID-19 visualizations would have been very helpful.
Part 03: Modes of Molecular Visualization
There are many mediums that provide 2D molecular visualizations. However, there are many typical problems associated with classic 2D interfaces, such as regular desktop computers, including, but not limited to, a lack of natural spatial understanding and interaction, as well as a limited field of view.
Immersive 3D visualizations can provide a more intuitive understanding of the molecular structure, its bonds, properties, and dynamics. In addition, With Oculus Quest headsets you don’t need cables and you don’t need to be physically attached to a computer, so you could roam from meeting room to meeting room and rapidly deploy the system with different teams. Such immersive environments ensure that different team members, who exhibit different expertise, areas of knowledge, and ways of knowing, are on the same page. When everyone is wearing headsets, everyone can view structures together and collaborate on them in real-time
While Nanome used to offer a desktop version of its platform, this is no longer the case!
Part 04: Comparable Models
Nanome seems to be the most user-friendly and technically rigorous molecular visualization platform out there. There are many other options available; However, many VR molecular visualization programs are expensive and challenging to use, work only on specific VR headsets, rely on complicated model-preparation software, and/or require the user to install separate programs or plugins. The section below looks at two, open source and publicly available, comparable models:
a web-based application that works on various VR setups and operating systems
displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space
ideal for hypothesis generation and education in research and large-classroom settings
available under the open-source BSD-3-Clause license
a copy of the program is available free of charge from http://durrantlab.com/protein-vr/, and a working version can be accessed at http://durrantlab.com/pvr/
an open-source software package where multiple users can cohabit in the same VR space and interact with real-time molecular simulations
it is based on the iMD-VR software framework and extends its functionality by enabling a multi-person VR experience, setting up and customizing interactive user manipulation with MD simulations, and running the application on a local network
via controlled studies in the laboratory, they demonstrated that Narupa and iMD-VR tools enable researchers to complete molecular modeling tasks more quickly than using conventional interfaces, such as a mouse or touchscreen
Other comparable models includes : PyMOL, ChimeraX, VMD, Maestro & Discovery Studio. These platforms offer many of the same features as Nanome, including advanced visualization options, protein structure analysis tools, and molecular docking capabilities. These are just a few examples of software packages that offer similar capabilities to Nanome. The choice of software will depend on the specific needs and preferences of the user, as well as the type of research or analysis being performed.
For a more comprehensive list of available comparable models, click here.